The traditional Chinese medicinal plant Desmodium styracifolium Merr. have efficient effect on preventing urinary calculi due to schaftoside. However, the schaftoside biosynthesis remains unknown. In this study, RNAseq transcriptomes and small RNAomes of leaves and flowers were sequenced and analyzed. There are 9955 differentially expressed genes DEGs and 86 differentially expressed microRNA miRNA identified. Pathway enrichment analysis show that phenylpropanoid biosynthesis and phenylalanine metabolism are over-represented in leaves when compared to flowers. A total of 30,934 simple sequence repeat SSR, 17,574 insertion-deletions InDels, and 86,882 single nucleotide polymorphisms SNPs were identified as gene-based markers. Schaftoside biosynthetic genes C-glucosyltransferase CGT and flavone synthase II FNSII and 1484 unigenes coexpressing with CGT and FNSII were predicted. Among them, 1038 unigenes containing gene-based marker coexpressed with CGT and 419 CGT-coexpressing unigenes can be successfully designed SSR markers. Moreover, 107 of 419 CGT-coexpressing unigenes containing SSR were randomly selected to validate the efficiency of SSR primers, which resulting 104 97.2 %) primers successfully amplified the polymerase chain reaction product and 54 (50.5 % primers are polymorphism primers. These results suggested that 211 polymorphic SSR markers could be further used for marker-assisted breeding MAB. Meanwhile, 6436 of 9955 DEGs containing gene-based marker differentially expressed in leaves when compared to flowers. Furthermore, 26 and 184 miRNA-targeted unigenes containing gene-based markers are CGT-coexpressing genes and DEGs, respectively. Candidate genes and gene-based markers identified in this study are useful resource, which lay a solid foundation for studying schaftoside biosynthesis, MAB, genetic map and comparative genomic study of D. styracifolium.

传统中草药金银花梅尔 具有有效的预防沙丁草胺引起的尿路结石的作用。然而，沙糖甙的生物合成仍然未知。在这项研究中，对叶片和花朵的RNAseq转录组和小RNAome进行了测序和分析。已鉴定出9955个差异表达的基因DEG和86个差异表达的microRNA miRNA。途径富集分析表明，与花相比，叶片中的苯丙烷生物合成和苯丙氨酸代谢过高。共有30,934个简单序列重复SSR，17,574个插入缺失InDels和86,882个单核苷酸多态性SNP被鉴定为基于基因的标记。预测了沙夫苷的生物合成基因C-葡萄糖基转移酶CGT和黄酮合酶II FNSII以及与CGT和FNSII共表达的1484个单基因。其中，可以成功设计包含与CGT共表达的基于基因的标记的1038个单基因和419个与CGT共表达的单基因的单基因。此外，从419个含有SSR的CGT共表达单基因中随机选择了107个，以验证SSR引物的效率，结果104个97.2％）引物成功扩增了聚合酶链反应产物，还有54个（50.5％的引物是多态性引物）。 211个多态性SSR标记可进一步用于标记辅助育种MAB；同时，与花相比，在9955个DEGs中有6436个含有基于基因的标记在叶中差异表达，此外，分别有26个和184个含基于基因的miRNA靶向单基因。 CGT共表达基因和DEGs，这项研究中确定的候选基因和基于基因的标记是有用的资源，D. styracifolium。